Differential relationship of fungal endophytic communities and metabolic profiling in the stems and roots of Ephedra sinica based on metagenomics and metabolomics

Fungal endophytic communities and metabolite profiles in the aerial and underground parts of plants differ exerting complex influences on each other through mechanisms that largely remain unknown. Ephedra sinica is a model for studying the interactions between endophytic fungi in different plant tissues that exhibit contrasting pharmacological activities. In this study, the endophytic fungal community and metabolites in the stems (Ea) and roots (Eb) of E. sinica were systematically investigated using metagenomic and metabolomic approaches, and their relationships were further analyzed. Results showed that OTU48 and OTU30589 were endophytic fungi shared by Ea and Eb, respectively. The genera of Phyllosticta fungi were specifically and abundantly present in Ea, whereas Talaromyces, Aporospora, and Aspergillus fungi were specific and abundant in Eb. A total of 17 significant differential metabolites were observed between Ea and Eb. Ephedrine and methylephedrine were mainly present in Ea, whereas ephedrannin A and mahuannin A were present in Eb. Nine endophytic fungi significantly (P < 0.05 or 0.01) correlated with several differential metabolites. The results of this study further substantiate the differential formation of secondary metabolites in specific plant tissues.